toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign,false);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";